Association of enteric shedding of bovine torovirus (Breda virus) and other enteropathogens with diarrhea in veal calves

Literature Review: Coinfection in Young Ruminant Livestock-Cryptosporidium spp. and Its Companions

The protozoan Cryptosporidium parvum is one of the major causative pathogens of diarrhoea in young ruminants; therefore, it causes economic losses and impairs animal welfare. Besides C. parvum, there are many other non-infectious and infectious factors, such as rotavirus, Escherichia coli, and Giardia duodenalis, which may lead to diarrhoeic disease in young livestock. Often, more than one infectious agent is detected in affected animals. Little is known about the interactions bet-ween simultaneously occurring pathogens and their potential effects on the course of disease. In this review, a brief overview about pathogens associated with diarrhoea in young ruminants is presented. Furthermore, information about coinfections involving Cryptosporidium is provided.

Development and use of a reverse transcription insulated isothermal PCR assay for detection and characterization of bovine torovirus in yaks

Bovine torovirus (BToV) is an important diarrhea-causing pathogen affecting bovines. To facilitate BToV detection, a reverse transcription insulated isothermal PCR (RT-iiPCR) assay was developed that targets the BToV M gene with high specificity and reproducibility. The assay has a limit of detection of 23 copies/μL. Out of 69 diarrheic fecal samples from yaks collected on six farms in Tibet and Sichuan provinces in China, 11.59% (8/69) tested positive for BToV using this assay. The full-length spike (S) and hemagglutinin-esterase (HE) genes of three positive samples were subsequently sequenced. Notably, an identical recombination event was identified in the S1 subunit of the S protein of three isolates. All of the HE genes were found to belong to genotype III and shared the same unique aa variation (P44S) in the esterase domain. This study is the first confirmation of BToV in yaks and the first report of an S gene recombination event in BToV. Our findings will enhance the current understanding of the molecular characteristics and genetic evolution of BToV.

Bovine Coronavirus and the Associated Diseases

Coronaviruses (CoVs) possess the largest and most complex RNA genome (up to 32 kb) that encodes for 16 non-structural proteins regulating RNA synthesis and modification. Coronaviruses are known to infect a wide range of mammalian and avian species causing remarkably diverse disease syndromes. Variable tissue tropism and the ability to easily cross interspecies barriers are the well-known characteristics of certain CoVs. The 21st century epidemics of severe acute respiratory CoV (SARS-CoV), Middle East respiratory CoV and the ongoing SARS-CoV-2 pandemic further highlight these characteristics and emphasize the relevance of CoVs to the global public health. Bovine CoVs (BCoVs) are betacoronaviruses associated with neonatal calf diarrhea, and with winter dysentery and shipping fever in older cattle. Of interest, no distinct genetic or antigenic markers have been identified in BCoVs associated with these distinct clinical syndromes. In contrast, like other CoVs, BCoVs exist as quasispecies. Besides cattle, BCoVs and bovine-like CoVs were identified in various domestic and wild ruminant species (water buffalo, sheep, goat, dromedary camel, llama, alpaca, deer, wild cattle, antelopes, giraffes, and wild goats), dogs and humans. Surprisingly, bovine-like CoVs also cannot be reliably distinguished from BCoVs using comparative genomics. Additionally, there are historical examples of zoonotic transmission of BCoVs. This article will discuss BCoV pathogenesis, epidemiology, interspecies transmission, immune responses, vaccines, and diagnostics.

Using routinely collected data to evaluate risk factors for mortality of veal calves

From 2009 to 2012 a gradual increase in on-farm mortality of Dutch veal calves was observed. In 2012, the cattle industry decided that more information was needed on risk factors for mortality in both veal herds and herds of origin to enable implementation of risk mitigating measures. Routinely collected data were available from seven different data sources and contained information from 2.4 million white veal calves that were fattened in the period between 1 January 2011 and 30 June 2014. Survival analysis techniques (Kaplan-Meier), multilevel Poisson and multilevel Logistic regression models were applied to analyse the data. Two different models were assembled in which risk factors for veal calf mortality in respectively veal herds and herds of origin were identified. Univariable and multivariable regression techniques were used to detect risk factors significantly associated with mortality of veal calves during the fattening period. During the study period, the mean mortality was 4.9% per production cycle. The probability to die was highest during the first weeks after arrival in the veal herds and declined thereafter. Important risk factors included a veal herds with a higher use of antimicrobials, hair colour as proxy for breed, certain countries of origin, veal herd management with a limited amount of supplied feed and a not having an all-in / all-out system. A higher body weight at arrival in the veal herd was associated with lower mortality as well as veal calves that were fed an above median amount of milk, roughage and concentrates. From the calves that were fattened during the study period, observations of 1.1 million calves originated from the Netherlands and were available to study risk factors for veal calf mortality associated with the herd of origin. Important risk factors included purchase, herds with high mortality rates in the quarter in which the calf was born, fast growth in herd size, high cattle replacement rates and a higher antibiotic use in the quarter of birth. Calves that originated from herds that were certified BVD-free, Salmonella-unsuspected or Paratuberculosis-unsuspected, had a lower odds to die during the subsequent fattening period in a veal herd. Veal calf mortality was influenced by risk factors at the herd of origin as well as at veal herds. Adequate collaboration between the different industries is necessary to optimize veal calf management leading to a reduction in veal calf mortality during the fattening period.

Detection and molecular characterisation of bovine corona and toroviruses from Croatian cattle

BACKGROUND

Bovine coronavirus (BCoV) together with bovine torovirus (BToV), both members of the Coronaviridae family, order Nidovirales are the most common viral enteric pathogens. Although studied separately, their joint occurrence and the molecular diversity in cattle in Croatia have not been investigated.

METHODS

A survey is carried out on 101 fecal samples from diarrheic young and adult cattle during the 3-year period from i) one large dairy herd, ii) four small herds and iii) three nasal and paired fecal samples from calves with symptoms of respiratory disease. Samples were submitted to RT-PCR and sequencing for BCoV Nucleocapsid gene, BCoV Spike gene and BToV Spike gene.

RESULTS

BCoV was detected in 78.8 % of fecal samples from symptomatic cattle and three nasal and paired fecal samples from calves with respiratory symptoms. BToV was detected in 43.2 % of fecal samples from symptomatic cattle and a fecal sample from calves with respiratory symptoms. Molecular characterisation of those viruses revealed some nucleotide and aminoacid differences in relation to reference strains.

CONCLUSIONS

BToV should be regarded as a relevant pathogen for cattle that plays a synergistic role in mixed enteric infections.

Genetic and antigenic analysis of Chlamydia pecorum strains isolated from calves with diarrhea

Chlamydia pecorum (designated 22-58) was isolated in 2010 in HmLu-1 cells from the jejunum of a calf which died of necrotizing enterocolitis in Yamaguchi Prefecture, Japan. Immunohistochemical staining identified C. pecorum positive reactions in the jejunal villi. C. pecorum, designated 24-100, was isolated from the feces of a calf with diarrhea in another farm in Yamaguchi Prefecture in 2012. A significant increase in neutralizing antibody titers against C. pecorum was confirmed in paired sera. Nucleotide sequence identities of omp1 genes of the 2 isolates were 100%. The isolates were genetically and antigenically more closely related to C. pecorum Bo/Yokohama strain isolated from cattle with enteritis in Japan than to the other prototype strains, Bo/Maeda isolated from cattle with pneumonia and Ov/IPA isolated from sheep with polyarthritis. These results indicate that C. pecorum strains similar to 22-58 and 24-100 might be endemic in Yamaguchi Prefecture and cause enteric disease in cattle.

Intestinal pathogens, diarrhoea and acute phase proteins in naturally infected dairy calves

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Multiple intestinal pathogen species were present in both healthy and diarrheic calves.

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Decreased haptoglobin concentrations were associated with weak signs of eimeriosis.

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Increased haptoglobin and fibrinogen concentrations were associated with respiratory tract infection and umbilical infection.

In this study, the association between Eimeria spp. related signs and innate immune response in dairy calves was examined. Calves (n = 100) aged 15–60 days were clinically examined and faecal samples, blood samples and deep nasopharyngeal swabs obtained. The samples were analysed for intestinal pathogens, acute phase proteins and WBC count, and respiratory tract pathogens, respectively.

Diarrhoea was diagnosed in 32.6% (23.3–43.0%, 95% CI) of calves. An association between the pathogenic Eimeria spp. and diarrhoea was detected by multiple correspondence analysis. Eimeria related signs (diarrhoea, presence of pathogenic species and total oocyst count) were combined resulting a four level variable. Calves with weak signs of eimeriosis had decreased haptoglobin concentrations (p = 0.02) and increased fibrinogen concentrations (p = 0.048) compared to no signs. Increased haptoglobin and fibrinogen concentrations were associated with respiratory tract infection and umbilical infection. Serum amyloid A and WBC counts showed no association with signs of eimeriosis or clinical diagnoses.

Toroviruses (Coronaviridae)

Toroviruses are single-stranded RNA peplomer-bearing enveloped viruses producing enteric disease in animals and humans. They have a unique extracellular C-shape or open torus morphology. There are four species in the genus Torovirus (family Coronaviridae, order Nidovirales): Equine torovirus (EToV), Bovine torovirus (BToV), Human torovirus (HToV), and Porcine torovirus (PToV), which have been reported worldwide. Their genome contains six ORFs, which are transcribed as a 3’-coterminal nested set of four mRNAs. ORF1a and 1b encode the replicase, and ORFs 2–5 encode the spike (S), membrane (M), hemagglutinin-esterase (HE), and nucleocapsid (N) proteins, respectively. Only EToVs and BToV Aichi/2004 propagate in cell culture.

Case-control study of microbiological etiology associated with calf diarrhea

Calf diarrhea is a major economic burden for the US cattle industry. A variety of infectious agents are implicated in calf diarrhea and co-infection of multiple pathogens is not uncommon in diarrheic calves. A case–control study was conducted to assess infectious etiologies associated with calf diarrhea in Midwest cattle farms. A total of 199 and 245 fecal samples were obtained from diarrheic and healthy calves, respectively, from 165 cattle farms. Samples were tested by a panel of multiplex PCR assays for 11 enteric pathogens: bovine rotavirus group A (BRV-A), bovine coronavirus (BCoV), bovine viral diarrhea virus (BVDV), bovine enterovirus (BEV), bovine norovirus (BNoV), Nebovirus, bovine torovirus (BToV) Salmonella spp. (Salmonella), Escherichia coli (E. coli) K99⁺, Clostridium perfringens with β toxin gene and Cryptosporidium parvum (C. parvum). The association between diarrhea and detection of each pathogen was analyzed using a multivariate logistic regression model. More than a half of the fecal samples from the diarrheic calves had multiple pathogens. Statistically, BRV-A, BCoV, BNoV, Nebovirus, Salmonella, E. coli K99⁺, and C. parvum were significantly associated with calf diarrhea (p < 0.05). Among them, C. parvum and BRV-A were considered to be the most common enteric pathogens for calf diarrhea with high detection frequency (33.7% and 27.1%) and strong odds ratio (173 and 79.9). Unexpectedly BNoV (OR = 2.0) and Nebovirus (OR = 16.7) were identified with high frequency in diarrheic calves, suggesting these viruses may have a significant contribution to calf diarrhea.

Evaluation of a commercial rapid test kit for detecting bovine enteric pathogens in feces

Recently a commercial antigen-capture enzyme-linked immunosorbent assay kit in the form of a dipstick (Bovine Enterichek®, Biovet Inc.) was made available to bovine practitioners and producers for the rapid detection of Betacoronavirus 1 (BCV-1), Rotavirus A (RV-A), Escherichia coli K99+, and Cryptosporidium parvum in feces from diarrheic calves. The diagnostic performance of Bovine Enterichek was evaluated in comparison with a multiplex real-time polymerase chain reaction assay (mrtPCR). One hundred fecal samples were procured from diagnostic submissions to Iowa State University Veterinary Diagnostic Laboratory and were used for the assessment. The agreement quotient (kappa) in results for each pathogen between Bovine Enterichek and mrtPCR were 0.095 (BCV-1), 0.521 (RV-A), 0.823 ( E. coli K99 +), and 0.840 ( C. parvum). In comparison to mrtPCR, the diagnostic sensitivity of Bovine Enterichek was 60.0%, 42.3%, 71.4%, and 81.5%, and the diagnostic specificity was 51.4%, 100%, 100%, and 98.6% for BCV-1, RV-A, E. coli K99 +, and C. parvum, respectively. The current study suggested that Bovine Enterichek can be a rapid test tool in the field for detection of RV-A, C. parvum, or E. coli K99+ in feces from calves at acute stage of clinical disease. However, test results for BCV-1 by the kit should be interpreted with caution due to low specificity and sensitivity of the kit.

Bovine coronavirus associated syndromes

Bovine coronaviruses, like other animal coronaviruses, have a predilection for intestinal and respiratory tracts. The viruses responsible for enteric and respiratory symptoms are closely related antigenically and genetically. Only 4 bovine coronavirus isolates have been completely sequenced and thus, the information about the genetics of the virus is still limited. This article reviews the clinical syndromes associated with bovine coronavirus, including pneumonia in calves and adult cattle, calf diarrhea, and winter dysentery; diagnostic methods; prevention using vaccination; and treatment, with adjunctive immunotherapy.

Detection and molecular characterization of porcine toroviruses in Korea

This study examined the prevalence and genetic diversity of the porcine torovirus (PToV) in Korea. Of 295 samples, 19 (6.4%) samples tested positive for PToVs by RT-PCR. A low nucleotide sequence identity of the partial S gene was detected among the Korean PToVs (73.5%) and between the Korean and European PToVs (74.0%). Phylogenetic analysis of the spike and nucleocapsid genes showed that the Korean PToVs form distinct branches with clusters corresponding to the farm of origin, which were separate from the other known foreign PToVs. These findings suggest that genetically diverse Korean PToV strains cause sporadic infections in Korea.

Pathophysiology of diarrhea in calves

Infectious diarrhea in calves is most commonly associated with enterotoxigenic Escherichia coli, Cryptosporidium parvum, rotavirus, coronavirus, or some combination of these pathogens. Each of these agents leads to diarrhea through either secretion or malabsorption/maldigestion, though the specific mechanisms and pathways may differ. Specific pharmacologic control and treatment are dependent on gaining a greater understanding of the pathophysiology of these organisms.

Disease management of dairy calves and heifers

This article focuses on the most important diseases of dairy calves and heifers and presents clinical approaches that can improve detection, diagnosis, and treatment of herd-based problems. A systematic herd investigation strategy is pivotal to define the problems, understand important risk factors, develop a plan, and make recommendations for disease management accurately. A review of records, colostrum and feeding routines, housing and bedding management, routine procedures, vaccination, and treatment protocols begins the investigation and determines which diagnostic procedures and testing strategies are most useful. Disease management is most effective when the problem source is well defined and the exposure can be limited, calf immunity can be enhanced, or a combination of both. Screening examinations performed regularly or done at strategic time points improves detection of disease, can be used to monitor treatment outcomes, and can avoid disease outbreaks.

Molecular epidemiology of bovine toroviruses circulating in South Korea

The prevalence of the bovine torovirus (BToV) and its genetic characterization have been reported in North America, Europe and Japan. Therefore, this study examined the prevalence and genetic diversity of the BToV in a total of 645 diarrheic fecal samples from 629 Korean native beef calf herds using RT-PCR and nested PCR with the primer pairs specific to a part of the BToV membrane (M) gene. Overall, 19 (2.9%) out of 645 diarrheic samples from 19 herds (6.9%) tested positive for BToVs by either RT-PCR or nested PCR. A comparison of the nucleotide (nt) and amino acid (aa) sequences of a part of the BToV M gene (409bp) among the BToVs showed the Korean BToVs to have comparatively higher sequence homology to the Japanese and Dutch BToVs than to the American and Italian BToVs. Generally, the Korean BToV strains clustered with the Japanese and Dutch BToV strains. However, the American and Italian BToV strains clustered on a separate major branch, suggesting that these are more distantly related to other known BToV strains. These results suggest that the BToV infections are sporadic in diarrheic calves in South Korea, and the Korean BToV strains are more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs.

Detection of bovine torovirus in fecal specimens of calves with diarrhea in Japan

The aim of this study was to determine the prevalence of bovine torovirus (BoTV) in bovine fecal samples and to determine whether a relationship exists between BoTV and diarrhea in Japan. Ninety-nine diarrheic and 114 normal fecal samples from calves in Hokkaido Prefecture and 38 diarrheic fecal samples from calves in 10 other prefectures were examined by reverse transcription (RT)-PCR with primers designed in the spike (S) gene for the presence of BoTV. The specimens were also examined for the presence of other enteric pathogens, bovine rotavirus, coronavirus and Cryptosporidium spp. BoTV RNA was detected in 15 (15.2%) of the 99 diarrheic samples from Hokkaido and in 9 (23.7%) of the 38 diarrheic samples from the other prefectures. The incidence of BoTV in control specimens was 7.0%. In 11 of the 15 BoTV-positive specimens from Hokkaido, BoTV was the only pathogen detected among those examined, and 11 BoTV-positive specimens were obtained from calves less than 2 weeks of age. Rotavirus was confirmed to be associated with calf diarrhea, but coronavirus and Cryptosporidium spp. were not. Nucleotide sequences of 17 different BoTV RT-PCR products were determined. Phylogenetic analysis based on the sequences revealed that Japanese BoTVs could be classified into at least two groups. This study showed that BoTV is a common virus in fecal specimens of calves with diarrhea in Japan and may be an important pathogen of cattle, principally in young calves less than 2 weeks of age.

Torovirus

Toroviruses are single-stranded RNA viruses with a peplomer-bearing envelope that have been associated with enteric disease in cattle and possibly humans. Toroviruses appear to occur worldwide, and torovirus-like particles in fecal preparations have been reported from Europe, the Americas, Asia, New Zealand, and South Africa. These viruses have a unique C-shape or open torus morphology in the extracellular environment. There are four recognized species in the genus Torovirus (family Coronaviridae, order Nidovirales): Equine torovirus, Bovine torovirus, Human torovirus, and Porcine torovirus. Among them there is little genetic divergence (20–40%). Antigenic cross-reactivity has revealed a relationship between equine torovirus (EToV), bovine torovirus (BToV), and human torovirus (HToV). The torovirus genome contains six open reading frames (ORFs), which are transcribed as a 3′ co-terminal nested set of four mRNAs. ORF1a and -1b encode the replicase, and ORFs 2–5 encode the spike (S), membrane (M), hemagglutinin-esterase (HE), and nucleocapsid (N) proteins, respectively. EToV is apathogenic, and the only torovirus that has been grown in vitro. All BToV strains are pathogenic, causing diarrhea in experimentally or naturally infected calves. HToVs have been associated with gastroenteritis and diarrhea in children, as well as with nosocomial infections in infants with necrotizing enterocolitis.

First isolation of cytopathogenic bovine torovirus in cell culture from a calf with diarrhea

A cytopathogenic virus (designated the Aichi/2004 strain) was isolated in a human rectal adenocarcinoma cell line (HRT-18) from the ileum contents of a calf with diarrhea. Oval and elongated particles, approximately 100 to 170 nm in diameter, with club-shaped projections were seen in the infected culture supernatant, and torovirus-like (tubular and torus nucleocapsid) structures were seen in the infected cells by electron microscopy. An antiserum against bovine torovirus (BToV) reacted with the infected cells by immunofluorescence and neutralized the isolate. However, antisera against bovine coronavirus (BCV) failed to react with the infected cells by immunofluorescence or did not neutralize the isolate. Further, the isolate was positive for BToV by reverse transcription-PCR (RT-PCR) targeting fragments of the nucleocapsid (N), membrane (M), and spike (S) genes. Comparison of the nucleotide sequences of the PCR products with those of the published N, M, and S genes (476 to 497, 672, and 687 to 690 nucleotides, respectively) of toroviruses showed high sequence identities (up to 99.4%, 98.7%, and 94.9% for the N, M, and S genes, respectively) between the isolate and BToVs. In contrast, the isolate was negative for BCV by RT-PCR. In a serological survey of serum samples from 355 calves at 33 farms, 92% of calves were positive for neutralizing antibodies to the isolate. These results indicate that the isolate in this study was BToV and that BToV infection might be common in cattle in Japan. To our knowledge, this is the first isolation of BToV in tissue culture.

Epidemiological analysis of bovine torovirus in Japan

Bovine torovirus (BToV), a member of the Coronaviridae family, is an established gastrointestinal infectious agent in cattle. No epidemiological research on BToV has been reported from Japan. In this study, we performed a survey to detect BToV in Japan in 2004 and 2005 using 231 fecal samples (167 from diarrheic cattle and 64 from asymptomatic cattle) that were analyzed by nested reverse transcription (RT) PCR using primers located in the consensus sequences of the reported BToV nucleocapsid (N), membrane (M), and spike (S) genes. BToV N, M, and S genes were detected in 6.5% (15/231), 6.1% (14/231), and 5.6% (13/231) of samples by nested-RT-PCR, respectively. In conclusion, detectability was improved compared to the results of the first round of RT-PCR. BToV was detected at a significantly higher rate in diarrheic samples than in asymptomatic samples (14/167 diarrheic samples [8.4%] and 1/64 asymptomatic samples [1.6%]), suggesting that BToV may act as a risk factor for diarrhea in Japanese cattle. The nucleotide sequence of M fragments from the BToV isolates including the newly identified Japanese isolates showed more than 97% identity. A similar degree of homology was observed in the N gene fragment among BToV isolates with the exception of BRV-1 and BRV-2. Domestic samples were classified into three clusters by phylogenetic analysis of the S gene fragment, which were considerably correlated with the geographic origin of the samples. BToV positive areas did not adjoin each other but were spread across a wide range, suggesting that BToV exists conventionally in Japan and is geographically differentiated. We also developed an RFLP method to distinguish these clusters using two restriction enzymes, HaeIII and AccI. This method should be useful for comparing newly acquired BToV-positive samples with the reported BToVs.

Detection of bovine torovirus in neonatal calf diarrhoea in Lower Austria and Styria (Austria)

Faeces of 230 calves with and without diarrhoea collected during the winter period 2004/2005 in 100 Austrian farms (Styria and Lower Austria) were examined for viral, bacterial and parasitic enteropathogens. Torovirus‐specific nucleic acid confirmed by reverse transcriptase‐polymerase chain reaction was found in 12 of 230 calves (5.2%). Ten of these calves were clinically ill, several of them showing signs of dehydration and abnormal faecal consistency at the time of sampling. Computer assisted analysis of two nucleotide sequences obtained from Austrian bovine samples revealed 93% similarity to Breda strain, but only 71% or 52% similarity to Equine Berne or Porcine Markelo torovirus strains respectively. Phylogenetic analysis grouped Austrian torovirus samples into the Bovine torovirus cluster indicating the first detection of Bovine torovirus in Austria. In addition, the following agents were detected in bovine faecal samples: Bovine coronavirus, 25.7%; Escherichia coli, 17%; Cryptosporidium spp., 11.7%; Eimeria spp., 10.4%; Rotavirus, 9.1%; Clostridium perfringens, 9.1% and Giardia spp., 6.1%. Salmonella spp. was not detected.

Bovine torovirus (Breda virus) revisited

Bovine torovirus (BoTV) is a pleomorphic virus with a spike-bearing envelope and a linear, non-segmented, positive-sense single-stranded RNA genome. This kidney-shaped virus is associated with diarrhea in calves and apparently has a worldwide distribution. This review provides details of the history and taxonomy of BoTV since its discovery in 1979. Information about virion morphology and architecture, antigenic and biological properties, viral genome, protein composition, thermal and chemical stability, and pH and proteolytic enzymes resistance is also summarized. A major focus of this review is to postulate a possible epidemiological cycle for BoTV, based on epidemiological data obtained in our studies and other published data, and progressing from the newborn calf to the adult animal. The distribution, host range, pathogenesis, disease and clinical signs (under experimental and natural exposure), pathology, diagnosis, prevention, treatment and control of BoTV infections are also described. In addition, a discussion of the zoonotic implications of torovirus-like particles detected in patients with gastroenteritis that resemble and cross-react with BoTV is presented. Hopefully, the findings described here will alert others to the existence of BoTV in cattle and its contribution to the diarrheal disease complex. This review also highlights the need for continual vigilance for potential zoonotic viruses belonging to the order Nidovirales, such as the SARS coronavirus.

The complete sequence of the bovine torovirus genome

Viruses in the family Coronaviridae have elicited new interest, with the outbreaks caused by SARS-HCoV in 2003 and the recent discovery of a new human coronavirus, HCoV-NL63. The genus Torovirus, within the family Coronaviridae, is less well characterized, in part because toroviruses cannot yet be grown in cell culture (except for the Berne virus). In this study, we determined the sequence of the complete genome of Breda-1 (BoTV-1), a bovine torovirus. This is the first complete torovirus genome sequence to be reported. BoTV-1 RNA was amplified using long RT-PCR and the amplicons sequenced. The genome has a length of 28.475 kb and consisted mainly of the replicase gene (∼20.2 kb) which contains two large overlapping ORFs, ORF1a and ORF1b, encoding polyproteins pp1a and pp1b, respectively. Sequence analysis identified conserved domains within the predicted sequences of pp1a and pp1b. Sequence alignments and protein secondary structure prediction data suggest the presence of a 3C-like serine protease domain with similarity to the arterivirus 3C-like serine protease and a single papain-like cysteine protease domain with similarity to the picornavirus leader protease. The ADRP (APPR-1″) domain – unique to the Coronaviridae – was also located in BoTV pp1a. In addition, several hydrophobic domains were identified that are typical of a nidovirus replicase. Within the pp1b sequence the polymerase and helicase domains were identified, as well as sequences predicted to be involved in ribosomal frameshifting, including the conserved slippery sequence UUUAAAC and two potential pseudoknot structures.